Gene expression data from 3D spheroids of human amniotic epithelial stem cell (hAESC) treated with 20 uM Carnosic Acid. Gene expression data from 3D spheroids of human amniotic epithelial stem cell (hAESC) treated with 20 uM Carnosic Acid

Gene expression profiling reveals multiple tissue-specific functionality of carnosic acid in a stem-based tool. We evaluated the effects of carnosic acid on human amniotic epithelial stem cells. We performed an untargeted whole-genome transcriptome analysis to explore functionality of carnosic acid in a stem cell-based tool. Overall design: According to the manufacturer's guide, the RNA was extracted using Isogen kit (Nip-pon Gene Co. Ltd., Japan). Then, RNA quantity and quality were determined using the NanoDrop 2000 spectrophotometer (ThermoScientific, USA). DNA microarray analysis was conducted on control and CA-treated hAESC samples using the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) and GeneChip™ Hybridization, Wash and Stain Kit (ThermoFisher Scientific) following the manufacturer's instructions. In brief, complementary DNA (cDNA) was synthesized from 100 ng of RNA solutions. cRNA was synthesized from in vitro transcription of cDNA and then purified and reverse transcribed. Finally, single-stranded cDNA (ss-cDNA) was synthesized, purified, fragmented, and labeled following the manufacturer's instructions. Cartridge Array Hybridization was performed using the Clariom S array (Human; ThermoFisher Scientific) on the GeneChip™ Fluidics Station (ThermoFisher Scientific). Scanning was performed using GeneChip Scanner (ThermoFisher Scientific). The raw image data obtained after scanning were analyzed using the Transcriptome Analysis Console (TAC) software (ver. 4.0.2, ThermoFisher Scientific). The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above back-ground (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7. Finally, genes that passed the filter criteria of p value 2 (in linear space) were considered as differentially expressed genes (DEGs).

基因表达谱分析揭示了鼠尾草酸（carnosic acid）在基于干细胞的工具中的多种组织特异性功能。本研究评估了鼠尾草酸对人羊膜上皮干细胞的影响，并通过非靶向全基因组转录组分析，探究鼠尾草酸在干细胞工具中的功能。总体实验设计：依照试剂盒制造商操作指南，采用Isogen试剂盒（日本Nippon Gene株式会社）提取总RNA。随后使用NanoDrop 2000分光光度计（美国赛默飞世尔科技，ThermoScientific）检测RNA的浓度与纯度。依照制造商操作说明，采用GeneChip WT PLUS试剂试剂盒（赛默飞世尔科技，ThermoFisher Scientific）与GeneChip™杂交、清洗与染色试剂盒（赛默飞世尔科技，ThermoFisher Scientific），对对照组与鼠尾草酸处理组的人羊膜上皮干细胞样本进行DNA微阵列分析。简言之，从100 ng RNA样品中合成互补脱氧核糖核酸（cDNA）；通过cDNA的体外转录合成互补核糖核酸（cRNA），随后对其进行纯化并逆转录。最后依照制造商操作流程，合成单链cDNA（ss-cDNA）并对其进行纯化、片段化与标记。在GeneChip™流体工作站（赛默飞世尔科技，ThermoFisher Scientific）上，采用Clariom S人源基因芯片（赛默飞世尔科技，ThermoFisher Scientific）进行芯片阵列杂交。使用GeneChip扫描仪（赛默飞世尔科技，ThermoFisher Scientific）完成芯片扫描。扫描得到的原始图像数据采用转录组分析控制台（TAC）软件（版本4.0.2，赛默飞世尔科技，ThermoFisher Scientific）进行分析。原始数据采用信号空间转换稳健多芯片分析（SST-RMA）算法进行标准化处理。随后采用Limma Bioconductor软件包进行基因水平分析。差异表达分析采用单因素方差分析（One-Way ANOVA）结合经验贝叶斯校正的方法完成。背景检测阈值（DABG）设为0.05。阳性/阴性曲线下面积（AUC）阈值设为≥0.7。最终，满足线性空间下p值阈值为2的筛选标准的基因被认定为差异表达基因（DEGs）。